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- PDB-6ihi: Crystal structure of RasADH 3B3/I91V from Ralstonia.sp in complex... -

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Basic information

Entry
Database: PDB / ID: 6ihi
TitleCrystal structure of RasADH 3B3/I91V from Ralstonia.sp in complex with NADPH and A6O
ComponentsAlclohol dehydrogenase
KeywordsHYDROLASE/INHIBITOR / OXIDOREDUCTASE / KRED / BIOCATALYST / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor / nucleotide binding
Similarity search - Function
: / PKS_KR / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-A6O / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Alclohol dehydrogenase/short-chain dehydrogenase
Similarity search - Component
Biological speciesRalstonia sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsZhang, H.L. / Chen, X. / Liu, W.D. / Wu, Q.Q. / Zhu, D.M.
CitationJournal: Nat Catal / Year: 2019
Title: Efficient reductive desymmetrization of bulky 1,3-cyclodiketones enabled by structure-guided directed evolution of a carbonyl reductase.
Authors: Chen, X. / Zhang, H.L. / Ma, M.S. / Liu, W. / Li, J. / Feng, J. / Liu, X. / Osuna, S. / Guo, R.T. / Wu, Q. / Zhu, D. / Ma, Y.
History
DepositionSep 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity_src_gen / struct / struct_keywords
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _struct.title / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alclohol dehydrogenase
B: Alclohol dehydrogenase
C: Alclohol dehydrogenase
D: Alclohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,4409
Polymers106,5814
Non-polymers2,8595
Water13,151730
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16380 Å2
ΔGint-88 kcal/mol
Surface area32020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.075, 69.075, 388.987
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 187 or resid 202 through 249))
21(chain B and resid 2 through 249)
31(chain C and (resid 2 through 187 or resid 202 through 249))
41(chain D and (resid 2 through 187 or resid 202 through 249))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRSERSER(chain A and (resid 2 through 187 or resid 202 through 249))AA2 - 1872 - 187
12ARGARGVALVAL(chain A and (resid 2 through 187 or resid 202 through 249))AA202 - 249202 - 249
21TYRTYRVALVAL(chain B and resid 2 through 249)BB2 - 2492 - 249
31TYRTYRSERSER(chain C and (resid 2 through 187 or resid 202 through 249))CC2 - 1872 - 187
32ARGARGVALVAL(chain C and (resid 2 through 187 or resid 202 through 249))CC202 - 249202 - 249
41TYRTYRSERSER(chain D and (resid 2 through 187 or resid 202 through 249))DD2 - 1872 - 187
42ARGARGVALVAL(chain D and (resid 2 through 187 or resid 202 through 249))DD202 - 249202 - 249

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Components

#1: Protein
Alclohol dehydrogenase


Mass: 26645.164 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia sp. (bacteria) / Plasmid: pET46Ek/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C0IR58
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-A6O / (2R,3S)-2-ethyl-2-[(2E)-2-(6-methoxy-3,4-dihydro-2H-naphthalen-1-ylidene)ethyl]-3-oxidanyl-cyclopentan-1-one


Mass: 314.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H26O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 730 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.33 % / Mosaicity: 0.263 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: LiCl, Bicine, PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2018
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→25 Å / Num. obs: 99773 / % possible obs: 99.9 % / Redundancy: 9 % / Biso Wilson estimate: 26.67 Å2 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.026 / Rrim(I) all: 0.079 / Χ2: 1.617 / Net I/σ(I): 9.3 / Num. measured all: 898880
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.849.30.76499870.8620.2630.8091.147100
1.84-1.929.30.529100050.9230.1820.561.194100
1.92-29.30.37199030.9650.1280.3931.318100
2-2.119.30.28599920.9770.0990.3011.494100
2.11-2.249.20.19299830.9870.0670.2031.632100
2.24-2.429.20.13699510.9930.0480.1441.49999.9
2.42-2.6690.1100320.9960.0350.1061.59699.9
2.66-3.048.50.08399500.9960.030.0882.29299.8
3.04-3.838.80.054100220.9980.0190.0582.13100
3.83-258.30.04199480.9990.0150.0432.00698.9

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BMS

4bms


Resolution: 1.78→24.708 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.45
RfactorNum. reflection% reflection
Rfree0.2143 2007 2.01 %
Rwork0.1848 --
obs0.1854 99646 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 126.07 Å2 / Biso mean: 32.5775 Å2 / Biso min: 15.47 Å2
Refinement stepCycle: final / Resolution: 1.78→24.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7204 0 190 730 8124
Biso mean--61.18 39.59 -
Num. residues----958
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2864X-RAY DIFFRACTION6.59TORSIONAL
12B2864X-RAY DIFFRACTION6.59TORSIONAL
13C2864X-RAY DIFFRACTION6.59TORSIONAL
14D2864X-RAY DIFFRACTION6.59TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7803-1.84390.29022050.260197749979100
1.8439-1.91770.26652050.237197929997100
1.9177-2.00490.23182040.212596929896100
2.0049-2.11060.24022050.208997759980100
2.1106-2.24270.2212020.198697759977100
2.2427-2.41570.24392050.200197349939100
2.4157-2.65860.24632050.1956982010025100
2.6586-3.04270.21241980.186497399937100
3.0427-3.83120.19391930.1716980710000100
3.8312-24.71050.1871850.16199731991699

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